Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 178 of 313
Found at i:55353629 original size:15 final size:15
Alignment explanation
Indices: 55353611--55353643 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
55353601 AAATTATACT
55353611 AAAATAAAA-AAAATG
1 AAAA-AAAAGAAAATG
55353626 AAAAAAAAGAAAATG
1 AAAAAAAAGAAAATG
55353641 AAA
1 AAA
55353644 TAAGTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (15 bp):
AAAAAAAAGAAAATG
Found at i:55354921 original size:76 final size:75
Alignment explanation
Indices: 55354795--55355018 Score: 279
Period size: 76 Copynumber: 2.9 Consensus size: 75
55354785 AAGGAGTGAT
* * *
55354795 TGATATTGTCGGTTTATCCGACTAGCGCCG-AGCGCAAATCTTCGTTGGTATATCCAACTAATGC
1 TGATATCGTCGGTTTATCCGACTAGCG--GTAGCGCAAATCTTCGTTGGTATATCAAACTAGTGC
55354859 TGGGCACATATC
64 TGGGCACATATC
* * *
55354871 TGATATCGTCGGTTTATCCGACTAACGGTATGCACAAATCTTTGTTGGTATATCAAACTAGTGCT
1 TGATATCGTCGGTTTATCCGACTAGCGGTA-GCGCAAATCTTCGTTGGTATATCAAACTAGTGCT
* * *
55354936 GGACACATGTT
65 GGGCACATATC
* * * * *
55354947 TGATATCGTCAGTTTATCCGACTAGTGATGGGCGCAAATCTTCGTTGGTATATCTAACTAGTGCT
1 TGATATCGTCGGTTTATCCGACTAGCGGT-AGCGCAAATCTTCGTTGGTATATCAAACTAGTGCT
55355012 GGGCACA
65 GGGCACA
55355019 AATCATTGTC
Statistics
Matches: 127, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
74 1 0.01
75 1 0.01
76 125 0.98
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (75 bp):
TGATATCGTCGGTTTATCCGACTAGCGGTAGCGCAAATCTTCGTTGGTATATCAAACTAGTGCTG
GGCACATATC
Found at i:55355083 original size:40 final size:36
Alignment explanation
Indices: 55354951--55355096 Score: 114
Period size: 36 Copynumber: 3.9 Consensus size: 36
55354941 CATGTTTGAT
* * * * *
55354951 ATCGTCAGTTTATCCGACTAGTGATGGGCGCAAATC
1 ATCGTCGGTTTATTCAACTAGTGCTGGGCACAAATC
* * *
55354987 TTCGTTGGTATA-TCTAACTAGTGCTGGGCACAAATC
1 ATCGTCGGTTTATTC-AACTAGTGCTGGGCACAAATC
* *
55355023 ATTGTCGGTTTATTCAACTAGTGCTGGGCACACATTTGAC
1 ATCGTCGGTTTATTCAACTAGTGCTGGGCACA-A-AT--C
** * *
55355063 ATCGTCGGTTTATTTGACTAGCGCTGGACACAAA
1 ATCGTCGGTTTATTCAACTAGTGCTGGGCACAAA
55355097 ACTTTGTTAC
Statistics
Matches: 85, Mismatches: 19, Indels: 10
0.75 0.17 0.09
Matches are distributed among these distances:
35 1 0.01
36 51 0.60
37 3 0.04
38 1 0.01
39 1 0.01
40 28 0.33
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (36 bp):
ATCGTCGGTTTATTCAACTAGTGCTGGGCACAAATC
Found at i:55361229 original size:26 final size:26
Alignment explanation
Indices: 55361200--55361353 Score: 159
Period size: 26 Copynumber: 5.9 Consensus size: 26
55361190 TTTAGTAGGT
*
55361200 TATGAGCCAGTGATTATTTAGCAAGC
1 TATGAGCCGGTGATTATTTAGCAAGC
* * *
55361226 TATGAGTCGTTGATTATTTAGCAGGC
1 TATGAGCCGGTGATTATTTAGCAAGC
* *
55361252 TATGAGCTGGTGTTTATTTAGCAAGC
1 TATGAGCCGGTGATTATTTAGCAAGC
* *
55361278 TTTGAGCCGGTGATTATTTAGCAGGCC
1 TATGAGCCGGTGATTATTTAGCAAG-C
* *
55361305 T-TGAGCTGGTAATTATTTCAGCAAGC
1 TATGAGCCGGTGATTATTT-AGCAAGC
* *
55361331 TTTGAGCTGGTGAATTA-TTAGCA
1 TATGAGCCGGTG-ATTATTTAGCA
55361354 GGTATTGTGT
Statistics
Matches: 107, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
26 85 0.79
27 18 0.17
28 4 0.04
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.36
Consensus pattern (26 bp):
TATGAGCCGGTGATTATTTAGCAAGC
Found at i:55361258 original size:52 final size:52
Alignment explanation
Indices: 55361174--55361355 Score: 206
Period size: 52 Copynumber: 3.5 Consensus size: 52
55361164 TTGTCAGGCC
* * * * **
55361174 TTGAGCCGATGATTTTTTTAGTAGGTTATGAGCCAGTGATTATTTAGCAAGCT
1 TTGAGCCGGTGA-TTATTTAGCAGGCTATGAGCTGGTGATTATTTAGCAAGCT
* * * *
55361227 ATGAGTCGTTGATTATTTAGCAGGCTATGAGCTGGTGTTTATTTAGCAAGCT
1 TTGAGCCGGTGATTATTTAGCAGGCTATGAGCTGGTGATTATTTAGCAAGCT
*
55361279 TTGAGCCGGTGATTATTTAGCAGGCCT-TGAGCTGGTAATTATTTCAGCAAGCT
1 TTGAGCCGGTGATTATTTAGCAGG-CTATGAGCTGGTGATTATTT-AGCAAGCT
*
55361332 TTGAGCTGGTGAATTA-TTAGCAGG
1 TTGAGCCGGTG-ATTATTTAGCAGG
55361356 TATTGTGTAC
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
52 70 0.63
53 37 0.33
54 4 0.04
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.37
Consensus pattern (52 bp):
TTGAGCCGGTGATTATTTAGCAGGCTATGAGCTGGTGATTATTTAGCAAGCT
Found at i:55365537 original size:18 final size:18
Alignment explanation
Indices: 55365514--55365550 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
55365504 GGAGTGCATT
55365514 ATATGAA-TGTGATAAGTG
1 ATATGAACT-TGATAAGTG
55365532 ATATGAACTTGATAAGTG
1 ATATGAACTTGATAAGTG
55365550 A
1 A
55365551 AAGTGTGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (18 bp):
ATATGAACTTGATAAGTG
Found at i:55372362 original size:25 final size:25
Alignment explanation
Indices: 55372325--55372375 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
55372315 TTGGGGGTAA
*
55372325 TAGGTCAATTGTTGGAAATCGCCAT
1 TAGGTCAACTGTTGGAAATCGCCAT
*
55372350 TAGGTCAACTGTTGGAAATCGTCAT
1 TAGGTCAACTGTTGGAAATCGCCAT
55372375 T
1 T
55372376 TTAGAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (25 bp):
TAGGTCAACTGTTGGAAATCGCCAT
Found at i:55377021 original size:10 final size:10
Alignment explanation
Indices: 55377006--55377032 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
55376996 TATTATTTAT
55377006 TTAATTTAAA
1 TTAATTTAAA
55377016 TTAATTTAAA
1 TTAATTTAAA
55377026 TTAATTT
1 TTAATTT
55377033 TTCAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTAATTTAAA
Found at i:55377046 original size:16 final size:17
Alignment explanation
Indices: 55377021--55377053 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
55377011 TTAAATTAAT
55377021 TTAAATTAATTTTTCAA
1 TTAAATTAATTTTTCAA
55377038 TTAAA-TAATTTTTCAA
1 TTAAATTAATTTTTCAA
55377054 CCTAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAATTAATTTTTCAA
Found at i:55394631 original size:15 final size:16
Alignment explanation
Indices: 55394606--55394635 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55394596 ATGACATTTA
55394606 TTTATTAAATAAAACT
1 TTTATTAAATAAAACT
55394622 TTTA-TAAATAAAAC
1 TTTATTAAATAAAAC
55394636 AATTTAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
TTTATTAAATAAAACT
Found at i:55395188 original size:20 final size:20
Alignment explanation
Indices: 55395163--55395200 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55395153 TAATTTTTCT
55395163 TTTTATACGAATTTTTATAA
1 TTTTATACGAATTTTTATAA
* *
55395183 TTTTATATGTATTTTTAT
1 TTTTATACGAATTTTTAT
55395201 TAAATCTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTATACGAATTTTTATAA
Found at i:55395862 original size:20 final size:22
Alignment explanation
Indices: 55395829--55395868 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
55395819 GTTATAAAAT
55395829 TAATTATATATATATTAAATAA
1 TAATTATATATATATTAAATAA
55395851 TAATTAT-T-TATATTAAAT
1 TAATTATATATATATTAAAT
55395869 TACTAACCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATTATATATATATTAAATAA
Found at i:55396019 original size:39 final size:39
Alignment explanation
Indices: 55395970--55396055 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 39
55395960 AAAATATATT
* * *
55395970 TAATACAATAAAATATTTATTATATTTATTTGT-GTTTTG
1 TAATATAATAAAACATTTATTATATTTA-TGGTAGTTTTG
* *
55396009 TAATATAATAAAACATTTATTGTATTTATGGTAGTTTTT
1 TAATATAATAAAACATTTATTATATTTATGGTAGTTTTG
55396048 TAATATAA
1 TAATATAA
55396056 ATATTTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
38 3 0.07
39 38 0.93
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.51
Consensus pattern (39 bp):
TAATATAATAAAACATTTATTATATTTATGGTAGTTTTG
Found at i:55397825 original size:26 final size:26
Alignment explanation
Indices: 55397796--55397845 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
55397786 AATTAGAGTA
*
55397796 AGAGTTAGAGAATTCCTTGATTTTCT
1 AGAGTTAGAGAATTCCTCGATTTTCT
*
55397822 AGAGTTAGAGAATTTCTCGATTTT
1 AGAGTTAGAGAATTCCTCGATTTT
55397846 GCTAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (26 bp):
AGAGTTAGAGAATTCCTCGATTTTCT
Found at i:55398924 original size:3 final size:3
Alignment explanation
Indices: 55398912--55398958 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
55398902 TATTATATAT
*
55398912 TAA TATA TAA TAA -AA TAA -AG TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
55398956 TAA
1 TAA
55398959 AGAATTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 3 0.08
3 33 0.85
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:55398989 original size:16 final size:16
Alignment explanation
Indices: 55398965--55399005 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
55398955 ATAAAGAATT
55398965 AAAAAGAAACA-AAGC
1 AAAAAGAAACAGAAGC
*
55398980 AAAAACGAAACAGAAGG
1 AAAAA-GAAACAGAAGC
55398997 AAAAAGAAA
1 AAAAAGAAA
55399006 GAAAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 8 0.35
ACGTcount: A:0.73, C:0.10, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAGAAACAGAAGC
Found at i:55399991 original size:25 final size:26
Alignment explanation
Indices: 55399963--55400051 Score: 71
Period size: 25 Copynumber: 3.5 Consensus size: 26
55399953 ATGAGCGTCT
55399963 CGATATATGGCT-TTTCGGAGCTTTC
1 CGATATATGGCTCTTTCGGAGCTTTC
** *
55399988 CGATGA-AAAGCTCTTTCACGAGC-TTC
1 CGAT-ATATGGCTCTTTC-GGAGCTTTC
* *
55400014 CTGAAATATGGCTCTTT-GGAGCTTCC
1 C-GATATATGGCTCTTTCGGAGCTTTC
55400040 CGATAT-TGGCTC
1 CGATATATGGCTC
55400052 GCTTGAACTT
Statistics
Matches: 49, Mismatches: 9, Indels: 13
0.69 0.13 0.18
Matches are distributed among these distances:
24 6 0.12
25 16 0.33
26 13 0.27
27 14 0.29
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (26 bp):
CGATATATGGCTCTTTCGGAGCTTTC
Found at i:55400116 original size:24 final size:23
Alignment explanation
Indices: 55400007--55400113 Score: 83
Period size: 24 Copynumber: 4.4 Consensus size: 23
55399997 GCTCTTTCAC
* *
55400007 GAGCTTCCTGAAATATGGCTCTTTG
1 GAGCTTCCCGATA-ATGGCTC-TTG
*
55400032 GAGCTTCCCGATATTGGCTCGCTT-
1 GAGCTTCCCGATAATGGCT--CTTG
* *
55400056 GAACTTCCCGATATTGGCTCGTAT-
1 GAGCTTCCCGATAATGGCTC-T-TG
*
55400080 GAGCTTCCCGTTAATGGCTCTTCG
1 GAGCTTCCCGATAATGGCTCTT-G
55400104 GAGCTTCCCG
1 GAGCTTCCCG
55400114 TTATACAGCT
Statistics
Matches: 69, Mismatches: 7, Indels: 13
0.78 0.08 0.15
Matches are distributed among these distances:
22 2 0.03
23 2 0.03
24 51 0.74
25 13 0.19
26 1 0.01
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (23 bp):
GAGCTTCCCGATAATGGCTCTTG
Found at i:55400149 original size:25 final size:25
Alignment explanation
Indices: 55400032--55400150 Score: 111
Period size: 24 Copynumber: 4.9 Consensus size: 25
55400022 TGGCTCTTTG
* *
55400032 GAGCTTCCCGATAT-TGGCTCGCTT
1 GAGCTTCCCGTTATATGGCTCGCAT
* * *
55400056 GAACTTCCCGATAT-TGGCTCGTAT
1 GAGCTTCCCGTTATATGGCTCGCAT
* *
55400080 GAGCTTCCCGTTA-ATGGCTCTTC-G
1 GAGCTTCCCGTTATATGGCTC-GCAT
** *
55400104 GAGCTTCCCGTTATACAGCTCACAT
1 GAGCTTCCCGTTATATGGCTCGCAT
55400129 GAGCTTCCCGTTATATGGCTCG
1 GAGCTTCCCGTTATATGGCTCG
55400151 AAAAAGCTTC
Statistics
Matches: 76, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
24 52 0.68
25 24 0.32
ACGTcount: A:0.17, C:0.29, G:0.23, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCGCAT
Found at i:55401792 original size:27 final size:27
Alignment explanation
Indices: 55401754--55401830 Score: 109
Period size: 27 Copynumber: 2.9 Consensus size: 27
55401744 CCCTGGGTGG
55401754 AGGGAAGCAGGTTGGCGGCACCAAACA
1 AGGGAAGCAGGTTGGCGGCACCAAACA
****
55401781 AGGGAAGCAGGTTGGCGGCACCAGTGG
1 AGGGAAGCAGGTTGGCGGCACCAAACA
*
55401808 AGGGAACCAGGTTGGCGGCACCA
1 AGGGAAGCAGGTTGGCGGCACCA
55401831 CCCTTGAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.27, C:0.22, G:0.42, T:0.09
Consensus pattern (27 bp):
AGGGAAGCAGGTTGGCGGCACCAAACA
Found at i:55401910 original size:10 final size:10
Alignment explanation
Indices: 55401879--55401950 Score: 63
Period size: 10 Copynumber: 6.6 Consensus size: 10
55401869 ATGAGAGGGG
*
55401879 AAGAAGAAGA
1 AAGAAAAAGA
55401889 AAGAAAGGAAGA
1 AAGAAA--AAGA
55401901 AAGAAAAAGA
1 AAGAAAAAGA
*
55401911 AGGAAAAAGA
1 AAGAAAAAGA
55401921 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
55401935 AAGAAAAAGA
1 AAGAAAAAGA
*
55401945 AGGAAA
1 AAGAAA
55401951 GAAAAGGAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
10 29 0.56
11 2 0.04
12 12 0.23
13 2 0.04
14 7 0.13
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:55401916 original size:14 final size:13
Alignment explanation
Indices: 55401882--55401955 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 13
55401872 AGAGGGGAAG
55401882 AAGAAGAAAG-AA
1 AAGAAGAAAGAAA
*
55401894 AGGAAGAAAGAAA
1 AAGAAGAAAGAAA
55401907 AAGAAGGAAAAAGAAA
1 AAGAA-G--AAAGAAA
55401923 GGAGAGGAAAGAAAGAAA
1 --A-A-G-AAGAAAGAAA
55401941 AAGAAGGAAAGAAA
1 AAGAA-GAAAGAAA
55401955 A
1 A
55401956 GGAAAGGGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
12 9 0.18
13 8 0.16
14 11 0.22
15 1 0.02
16 8 0.16
18 8 0.16
19 1 0.02
20 2 0.04
21 2 0.04
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAGAAA
Found at i:55401919 original size:28 final size:30
Alignment explanation
Indices: 55401879--55401954 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 30
55401869 ATGAGAGGGG
55401879 AAGAAGAAGAAAGAAAGGA-A-GAAAGAAA
1 AAGAAGAAGAAAGAAAGGAGAGGAAAGAAA
55401907 AAGAAGGAA-AAAGAAAGGAGAGGAAAGAAA
1 AAGAA-GAAGAAAGAAAGGAGAGGAAAGAAA
*
55401937 GAAAAAGAAGGAAAGAAA
1 -AAGAAGAA-GAAAGAAA
55401955 AGGAAAGGGG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
28 15 0.37
29 4 0.10
30 11 0.27
31 4 0.10
32 7 0.17
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (30 bp):
AAGAAGAAGAAAGAAAGGAGAGGAAAGAAA
Found at i:55401955 original size:38 final size:37
Alignment explanation
Indices: 55401877--55401985 Score: 129
Period size: 38 Copynumber: 3.1 Consensus size: 37
55401867 GAATGAGAGG
* *
55401877 GGAAGAAGAAGAAA-GAAAGG-AAGAAAGAAAAAGAA
1 GGAAGAAAAAGAAAGGAGAGGAAAGAAAGAAAAAGAA
55401912 -G--GAAAAAGAAAGGAGAGGAAAGAAAGAAAAAGAA
1 GGAAGAAAAAGAAAGGAGAGGAAAGAAAGAAAAAGAA
* * *
55401946 GGAAAGAAAAGGAAAGGGGAGGAAAGAAAGAAAAATAA
1 GG-AAGAAAAAGAAAGGAGAGGAAAGAAAGAAAAAGAA
55401984 GG
1 GG
55401986 CGTTTGAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
32 9 0.14
33 5 0.08
34 16 0.25
35 1 0.02
38 32 0.51
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (37 bp):
GGAAGAAAAAGAAAGGAGAGGAAAGAAAGAAAAAGAA
Found at i:55401957 original size:10 final size:10
Alignment explanation
Indices: 55401899--55401961 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
55401889 AAGAAAGGAA
*
55401899 GAAAGAAAAA
1 GAAAGAAAAG
* *
55401909 GAAGGAAAAA
1 GAAAGAAAAG
* *
55401919 GAAAGGAGAG
1 GAAAGAAAAG
55401929 GAAAG-AAA-
1 GAAAGAAAAG
55401937 GAAA-AAGAAG
1 GAAAGAA-AAG
55401947 GAAAGAAAAG
1 GAAAGAAAAG
55401957 GAAAG
1 GAAAG
55401962 GGGAGGAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
8 5 0.12
9 4 0.09
10 32 0.74
11 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:55401958 original size:28 final size:28
Alignment explanation
Indices: 55401882--55401961 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
55401872 AGAGGGGAAG
55401882 AAGAA-GAAAG-AAAGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
55401907 AAGAAGGAAAAAGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG--AAAG-AA--A-AGGAAAGAAAGAAA
55401941 AAGAAGGAAAGAAAAGGAAAG
1 AAGAAGGAAAGAAAAGGAAAG
55401962 GGGAGGAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
28 11 0.24
29 1 0.02
30 1 0.02
31 2 0.04
32 5 0.11
33 3 0.07
34 17 0.37
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:55402139 original size:68 final size:68
Alignment explanation
Indices: 55402059--55402211 Score: 306
Period size: 68 Copynumber: 2.2 Consensus size: 68
55402049 TAATGCAACT
55402059 TTAAAATAATTAAATTGGTAAAAAGAAATTGAACAATAAGCACAATAACTAAAACTAGAGTAATT
1 TTAAAATAATTAAATTGGTAAAAAGAAATTGAACAATAAGCACAATAACTAAAACTAGAGTAATT
55402124 AAA
66 AAA
55402127 TTAAAATAATTAAATTGGTAAAAAGAAATTGAACAATAAGCACAATAACTAAAACTAGAGTAATT
1 TTAAAATAATTAAATTGGTAAAAAGAAATTGAACAATAAGCACAATAACTAAAACTAGAGTAATT
55402192 AAA
66 AAA
55402195 TTAAAATAATTAAATTG
1 TTAAAATAATTAAATTG
55402212 ATACAAAAAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 85 1.00
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.27
Consensus pattern (68 bp):
TTAAAATAATTAAATTGGTAAAAAGAAATTGAACAATAAGCACAATAACTAAAACTAGAGTAATT
AAA
Found at i:55404980 original size:25 final size:25
Alignment explanation
Indices: 55404927--55404980 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
55404917 ATTTAGTGTG
*
55404927 TTTTTTTCTCTTTTTTATTTTTAT-
1 TTTTTTTCTCTTTTTTATTTATATA
*
55404951 TTTTTTTTTACTTTTTT-TTTGATATA
1 TTTTTTTCT-CTTTTTTATTT-ATATA
55404977 TTTT
1 TTTT
55404981 GGTAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 11 0.44
25 10 0.40
26 4 0.16
ACGTcount: A:0.11, C:0.06, G:0.02, T:0.81
Consensus pattern (25 bp):
TTTTTTTCTCTTTTTTATTTATATA
Found at i:55405002 original size:27 final size:29
Alignment explanation
Indices: 55404972--55405041 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
55404962 TTTTTTTTTG
55404972 ATATATTTTGGTAAAT-AAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
55404999 ATATATTTTGGTAAATAAAAAAAAAGTTAT
1 ATATATTTTGGTAAAT-AAAAAAAAGTTAT
55405029 A-ATATTTTGGTAA
1 ATATATTTTGGTAA
55405042 TTTTTTATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
27 16 0.40
29 19 0.47
30 5 0.12
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAAGTTAT
Found at i:55405105 original size:18 final size:18
Alignment explanation
Indices: 55405084--55405119 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55405074 AACCCAGTAC
*
55405084 AAAAATAATAAAATATTA
1 AAAAATAACAAAATATTA
*
55405102 AAAAATACCAAAATATTA
1 AAAAATAACAAAATATTA
55405120 TATATATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAATAACAAAATATTA
Found at i:55405860 original size:34 final size:34
Alignment explanation
Indices: 55405790--55405905 Score: 105
Period size: 35 Copynumber: 3.3 Consensus size: 34
55405780 ATTACCTTAT
55405790 TTTCTTTTTTTTTCCTTC-CTTC-CCTCTT-CTTCTTC
1 TTTCTTTTTTTTT--TTCTCTTCTCCT-TTCCTT-TTC
55405825 TTTCTTTTTTTTTTTCTCTTCTCCTTTCCTTTTC
1 TTTCTTTTTTTTTTTCTCTTCTCCTTTCCTTTTC
*
55405859 TTTCCTTATTTTTCTTTCT-TTCCTCCCCTTTCCTTTTC
1 TTT-CTT-TTTTTTTTTCTCTT-CT--CCTTTCCTTTTC
*
55405897 CTTCTTTTT
1 TTTCTTTTT
55405906 CTTTCTCCCT
Statistics
Matches: 71, Mismatches: 2, Indels: 15
0.81 0.02 0.17
Matches are distributed among these distances:
33 3 0.04
34 12 0.17
35 24 0.34
36 15 0.21
37 3 0.04
38 14 0.20
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (34 bp):
TTTCTTTTTTTTTTTCTCTTCTCCTTTCCTTTTC
Found at i:55405871 original size:38 final size:39
Alignment explanation
Indices: 55405784--55405902 Score: 102
Period size: 38 Copynumber: 3.0 Consensus size: 39
55405774 ATAAAAATTA
* * *
55405784 CCTTATTTTCTTTTTTTTTC-CTTCCTTCCCTCTTCTTCTT
1 CCTTATTTT-TTTTTTTCTCTC-TCCTTTCCTTTTCTTCTT
* *
55405824 CTTTCTTTTTTTTTTTCTCTTCTCCTTTCCTTTTC-T-TT
1 CCTTATTTTTTTTTTTCTC-TCTCCTTTCCTTTTCTTCTT
*
55405862 CCTTATTTTTCTTTCTTTC-CTCCCCTTTCCTTTTCCTTCTT
1 CCTTATTTTT-TTT-TTTCTCTCTCCTTTCCTTTT-CTTCTT
55405903 TTTCTTTCTC
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
38 23 0.36
39 15 0.23
40 23 0.36
41 3 0.05
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (39 bp):
CCTTATTTTTTTTTTTCTCTCTCCTTTCCTTTTCTTCTT
Found at i:55405928 original size:28 final size:31
Alignment explanation
Indices: 55405855--55405931 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 31
55405845 CTCCTTTCCT
* *
55405855 TTTCTTTCCTTATTTTTCTTTCTTTCCTCCCC
1 TTTCTTT-CTTCTTCTTCTTTCTTTCCTCCCC
*
55405887 TTTCCTTT-TCCTTCTT-TTTCTTT-CT-CCC
1 TTT-CTTTCTTCTTCTTCTTTCTTTCCTCCCC
55405915 TTTCTTTCTTCTTCTTC
1 TTTCTTTCTTCTTCTTC
55405932 CCCTCTCCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
27 4 0.11
28 13 0.34
29 2 0.05
30 7 0.18
31 5 0.13
32 3 0.08
33 4 0.11
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (31 bp):
TTTCTTTCTTCTTCTTCTTTCTTTCCTCCCC
Found at i:55406084 original size:17 final size:17
Alignment explanation
Indices: 55406062--55406102 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
55406052 GTTCAGGTTT
55406062 TTTTTTTCTGTTTTTTA
1 TTTTTTTCTGTTTTTTA
*
55406079 TTTTTTTCTGTTTTTTG
1 TTTTTTTCTGTTTTTTA
55406096 TTTTTTT
1 TTTTTTT
55406103 TGGTAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.85
Consensus pattern (17 bp):
TTTTTTTCTGTTTTTTA
Found at i:55408222 original size:21 final size:22
Alignment explanation
Indices: 55408198--55408246 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
55408188 TTATTTTGTC
*
55408198 TTTTTAAAAATTAATTTTA-AT
1 TTTTTAAAAATTAACTTTAGAT
* * *
55408219 TTTTTTAGAATTAACTTTAGGT
1 TTTTTAAAAATTAACTTTAGAT
55408241 TTTTTA
1 TTTTTA
55408247 GTAAAAGGGA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (22 bp):
TTTTTAAAAATTAACTTTAGAT
Found at i:55412535 original size:21 final size:21
Alignment explanation
Indices: 55412506--55412546 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
55412496 AGTCGTTGGT
*
55412506 AGGCTATGTCTCGAGACATGC
1 AGGCCATGTCTCGAGACATGC
55412527 AGGCCATGTCTCGAGACATG
1 AGGCCATGTCTCGAGACATG
55412547 TAGCCCCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (21 bp):
AGGCCATGTCTCGAGACATGC
Found at i:55414788 original size:13 final size:13
Alignment explanation
Indices: 55414772--55414813 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
55414762 AAATCTCAAA
55414772 ATTTACTTATAAT
1 ATTTACTTATAAT
* *
55414785 ATTTA-ATAT-GT
1 ATTTACTTATAAT
55414796 ATTTACTTATAAT
1 ATTTACTTATAAT
55414809 ATTTA
1 ATTTA
55414814 AAAAAATTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
11 6 0.26
12 6 0.26
13 11 0.48
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (13 bp):
ATTTACTTATAAT
Found at i:55422555 original size:15 final size:15
Alignment explanation
Indices: 55422499--55422556 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
55422489 ATAAATTTTG
* *
55422499 CAGCACCTACAACTA
1 CAGCAACTACGACTA
** *
55422514 CAGCAACTGTGACAA
1 CAGCAACTACGACTA
* *
55422529 CAGCGACAACGACTA
1 CAGCAACTACGACTA
55422544 CAGCAACTACGAC
1 CAGCAACTACGAC
55422557 AGCAGCAAGA
Statistics
Matches: 31, Mismatches: 12, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.40, C:0.34, G:0.16, T:0.10
Consensus pattern (15 bp):
CAGCAACTACGACTA
Found at i:55425799 original size:4 final size:4
Alignment explanation
Indices: 55425790--55425816 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
55425780 CAAAACCAGC
55425790 AGTG AGTG AGTG AGTG AGTG AGTG AGT
1 AGTG AGTG AGTG AGTG AGTG AGTG AGT
55425817 CAGAGGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.48, T:0.26
Consensus pattern (4 bp):
AGTG
Found at i:55427349 original size:14 final size:14
Alignment explanation
Indices: 55427330--55427360 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55427320 AACATTTTAA
*
55427330 TGGAATGTAATTTT
1 TGGAATGTAATTGT
55427344 TGGAATGTAATTGT
1 TGGAATGTAATTGT
55427358 TGG
1 TGG
55427361 GGGAAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (14 bp):
TGGAATGTAATTGT
Found at i:55436037 original size:44 final size:44
Alignment explanation
Indices: 55435974--55436064 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
55435964 ACTCATCATG
55435974 GGCGATAGACTGTGGAGGCCTCCATGAGCATTTTTATGAGCTTA
1 GGCGATAGACTGTGGAGGCCTCCATGAGCATTTTTATGAGCTTA
55436018 GGCGATAGACTGTGGAGGCCTCCATGAGCATTTTTATGAGCTTA
1 GGCGATAGACTGTGGAGGCCTCCATGAGCATTTTTATGAGCTTA
55436062 GGC
1 GGC
55436065 TATAATGGGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.29
Consensus pattern (44 bp):
GGCGATAGACTGTGGAGGCCTCCATGAGCATTTTTATGAGCTTA
Found at i:55436385 original size:27 final size:27
Alignment explanation
Indices: 55436354--55436440 Score: 131
Period size: 27 Copynumber: 3.2 Consensus size: 27
55436344 CTAAAATATA
* *
55436354 TAAAATGACCAAAATACCCTCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
55436381 TAAAATGACCGAAATACCCCCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
*
55436408 TAAAATGATCGAAATACCCCCACT-GGG
1 TAAAATGACCGAAATACCCCCA-TAGGG
55436435 TAAAAT
1 TAAAAT
55436441 ACCTTATAGG
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
27 55 0.98
28 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCCCATAGGG
Found at i:55436511 original size:71 final size:72
Alignment explanation
Indices: 55436364--55436497 Score: 198
Period size: 71 Copynumber: 1.9 Consensus size: 72
55436354 TAAAATGACC
* *
55436364 AAAATACCCTCATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCC
1 AAAATACCCTCATAGGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCC
55436429 ACTGGGT
66 ACTGGGT
* ** * *
55436436 AAAATA-CCTTATAGGGTAAAATAATTGAAATACCCTCGTAGGGTAAAATGACCGAAATACCC
1 AAAATACCCTCATAGGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCC
55436498 TTATAGGGTA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
71 49 0.89
72 6 0.11
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (72 bp):
AAAATACCCTCATAGGGTAAAATAACCGAAATACCCCCATAGGGTAAAATGACCGAAATACCCCC
ACTGGGT
Found at i:55436512 original size:27 final size:27
Alignment explanation
Indices: 55436437--55436514 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
55436427 CCACTGGGTA
* **
55436437 AAATA-CCTTATAGGGTAAAATAATTG
1 AAATACCCTTATAGGGTAAAATGACCG
**
55436463 AAATACCCTCGTAGGGTAAAATGACCG
1 AAATACCCTTATAGGGTAAAATGACCG
55436490 AAATACCCTTATAGGGTAAAATGAC
1 AAATACCCTTATAGGGTAAAATGAC
55436515 TATTATACCC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 5 0.11
27 39 0.89
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (27 bp):
AAATACCCTTATAGGGTAAAATGACCG
Found at i:55436522 original size:27 final size:26
Alignment explanation
Indices: 55436437--55436527 Score: 94
Period size: 27 Copynumber: 3.4 Consensus size: 26
55436427 CCACTGGGTA
* *
55436437 AAATA-CCTTATAGGGTAAAATAATT
1 AAATACCCTTATAGGGTAAAATGACT
** *
55436462 GAAATACCCTCGTAGGGTAAAATGACCG
1 -AAATACCCTTATAGGGTAAAATGA-CT
55436490 AAATACCCTTATAGGGTAAAATGACT
1 AAATACCCTTATAGGGTAAAATGACT
*
55436516 ATTATACCCTTA
1 A-AATACCCTTA
55436528 AGAGATGAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
26 7 0.13
27 46 0.87
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.27
Consensus pattern (26 bp):
AAATACCCTTATAGGGTAAAATGACT
Found at i:55442612 original size:13 final size:12
Alignment explanation
Indices: 55442596--55442634 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
55442586 TTACAGTTAA
55442596 AGATAACAGAATC
1 AGATAACAGAA-C
55442609 AGATAAGCAGAAC
1 AGATAA-CAGAAC
55442622 AGATATACAGAAC
1 AGATA-ACAGAAC
55442635 CCTACCCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.54, C:0.15, G:0.18, T:0.13
Consensus pattern (12 bp):
AGATAACAGAAC
Found at i:55444706 original size:37 final size:37
Alignment explanation
Indices: 55444664--55444737 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
55444654 TGCACATTTT
* *
55444664 CACTTATACCCACCTATGCCGGATGCATACATATATA
1 CACTTATACCCACCTATGCCGAATGCATACAAATATA
* *
55444701 CACTTATATCTACCTATGCCGAATGCATACAAATATA
1 CACTTATACCCACCTATGCCGAATGCATACAAATATA
55444738 TATCCACCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.28
Consensus pattern (37 bp):
CACTTATACCCACCTATGCCGAATGCATACAAATATA
Found at i:55445000 original size:41 final size:41
Alignment explanation
Indices: 55444950--55445043 Score: 152
Period size: 41 Copynumber: 2.3 Consensus size: 41
55444940 AATTCATCAT
* *
55444950 ATTCGGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
55444991 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
*
55445032 ATTCAAATCACC
1 ATTCAGATCACC
55445044 AATTNCTCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTG
Found at i:55445097 original size:71 final size:70
Alignment explanation
Indices: 55444980--55445114 Score: 234
Period size: 71 Copynumber: 1.9 Consensus size: 70
55444970 GCCTGCTAGG
*
55444980 CTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAAATCACCA
1 CTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAAATCACCA
55445045 ATTNCT
66 ATT-CT
* *
55445051 CTTATAGCCTGATTCATATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAATCACC
1 CTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAAATCACC
55445115 GGCACTTAGC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (70 bp):
CTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAAATCACCA
ATTCT
Found at i:55445113 original size:41 final size:41
Alignment explanation
Indices: 55445051--55445155 Score: 165
Period size: 41 Copynumber: 2.6 Consensus size: 41
55445041 ACCAATTNCT
* *
55445051 CTTATAGCCTGATTCATATCACCGGCACTTAGCCTGCTAGG
1 CTTATAGCCTGATTCAAATCACCGGCACTTAGCCTGCTAGA
55445092 CTTATAGCCTGATTCAAATCACCGGCACTTAGCCTGCTAGA
1 CTTATAGCCTGATTCAAATCACCGGCACTTAGCCTGCTAGA
* * *
55445133 TTTATAACCTGATTCAATTCACC
1 CTTATAGCCTGATTCAAATCACC
55445156 AATTCCAAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (41 bp):
CTTATAGCCTGATTCAAATCACCGGCACTTAGCCTGCTAGA
Found at i:55445155 original size:112 final size:111
Alignment explanation
Indices: 55444956--55445160 Score: 374
Period size: 112 Copynumber: 1.8 Consensus size: 111
55444946 TCATATTCGG
* *
55444956 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAATCACCGGCACTTAGCCTGCTAGA
55445021 TTTATAACCTGATTCAAATCACCAATTNCTCTTATAGCCTGATTCAT
66 TTTATAACCTGATTCAAATCACCAATT-CTCTTATAGCCTGATTCAT
55445068 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAATCACCGGCACTTAGCCTGCTAGA
1 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAATCACCGGCACTTAGCCTGCTAGA
*
55445133 TTTATAACCTGATTCAATTCACCAATTC
66 TTTATAACCTGATTCAAATCACCAATTC
55445161 CAAACTTAAA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
111 1 0.01
112 89 0.99
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (111 bp):
ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAAATCACCGGCACTTAGCCTGCTAGA
TTTATAACCTGATTCAAATCACCAATTCTCTTATAGCCTGATTCAT
Found at i:55445396 original size:19 final size:19
Alignment explanation
Indices: 55445369--55445405 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55445359 TTGTTCGATC
* *
55445369 CACATATATATATATATTA
1 CACACATATACATATATTA
55445388 CACACATATACATATATT
1 CACACATATACATATATT
55445406 CGCACATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.38
Consensus pattern (19 bp):
CACACATATACATATATTA
Found at i:55465103 original size:16 final size:17
Alignment explanation
Indices: 55465071--55465103 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55465061 ATCACAATAA
55465071 AATAAAATTCTAATATT
1 AATAAAATTCTAATATT
55465088 AATAAAATT-TAATATT
1 AATAAAATTCTAATATT
55465104 TTCATATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAAAATTCTAATATT
Found at i:55467441 original size:22 final size:21
Alignment explanation
Indices: 55467406--55467482 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 21
55467396 AAAAGGTATC
* * *
55467406 TACAAATTAAATCTCTAATAT
1 TACAAATCATATCTCTAAGAT
55467427 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
55467450 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
55467469 TACATATCATATCT
1 TACAAATCATATCT
55467483 AAGATTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 18 0.39
21 4 0.09
22 15 0.33
23 9 0.20
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:55467466 original size:19 final size:19
Alignment explanation
Indices: 55467442--55467495 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
55467432 AATCATATCT
55467442 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
55467461 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
55467480 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
55467496 CTTGAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:55467880 original size:18 final size:18
Alignment explanation
Indices: 55467849--55467898 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
55467839 TATATTATAA
55467849 TATTAATTAATAAAATAT
1 TATTAATTAATAAAATAT
* *
55467867 TATTACTTATTAAAATAT
1 TATTAATTAATAAAATAT
55467885 TATTAA-TAATAAAA
1 TATTAATTAATAAAA
55467899 ACATCATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTAATTAATAAAATAT
Found at i:55469278 original size:27 final size:27
Alignment explanation
Indices: 55469240--55469295 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
55469230 TGGTATATAA
55469240 TAAAGGAGAGTTCAGCCATAATACTTC
1 TAAAGGAGAGTTCAGCCATAATACTTC
* *
55469267 TAAAGGAGAGTTTAGTCATAATACTTC
1 TAAAGGAGAGTTCAGCCATAATACTTC
55469294 TA
1 TA
55469296 GTGGGGTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (27 bp):
TAAAGGAGAGTTCAGCCATAATACTTC
Found at i:55469584 original size:21 final size:21
Alignment explanation
Indices: 55469545--55469584 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
55469535 TTAAGAATTA
*
55469545 ATTTAATTTCATTGGATTATT
1 ATTTAATTTCATTGAATTATT
55469566 ATTTAATTT-ATTGTAATTA
1 ATTTAATTTCATTG-AATTA
55469585 AATAATTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (21 bp):
ATTTAATTTCATTGAATTATT
Found at i:55472727 original size:23 final size:23
Alignment explanation
Indices: 55472700--55472754 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
55472690 AAACTAATCC
55472700 TCTCTCAAATTTCCTCTC-AATT
1 TCTCTCAAATTTCCTCTCAAATT
*
55472722 TGCTCTCAAA-TTCCTTTCAAATT
1 T-CTCTCAAATTTCCTCTCAAATT
55472745 TCTCTCAAAT
1 TCTCTCAAAT
55472755 CCATATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 16 0.55
23 13 0.45
ACGTcount: A:0.25, C:0.29, G:0.02, T:0.44
Consensus pattern (23 bp):
TCTCTCAAATTTCCTCTCAAATT
Found at i:55472753 original size:11 final size:11
Alignment explanation
Indices: 55472700--55472754 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
55472690 AAACTAATCC
55472700 TCTCTCAAATT
1 TCTCTCAAATT
55472711 TCCTCTC-AATT
1 T-CTCTCAAATT
55472722 TGCTCTCAAATT
1 T-CTCTCAAATT
* *
55472734 CCTTTCAAATT
1 TCTCTCAAATT
55472745 TCTCTCAAAT
1 TCTCTCAAAT
55472755 CCATATTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.25, C:0.29, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:55472804 original size:11 final size:12
Alignment explanation
Indices: 55472769--55472805 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
55472759 ATTTAATCTC
55472769 AATTTACTCTT-
1 AATTTACTCTTA
*
55472780 AATTTCCTCTTA
1 AATTTACTCTTA
55472792 AATTT-CTCTTA
1 AATTTACTCTTA
55472803 AAT
1 AAT
55472806 CCCCATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (12 bp):
AATTTACTCTTA
Found at i:55473969 original size:7 final size:7
Alignment explanation
Indices: 55473957--55473988 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
55473947 AGTCGATTGT
55473957 TATTTAG
1 TATTTAG
55473964 TATTTAG
1 TATTTAG
55473971 TATTTAG
1 TATTTAG
55473978 TATTTAG
1 TATTTAG
55473985 TATT
1 TATT
55473989 ATGTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (7 bp):
TATTTAG
Found at i:55474663 original size:18 final size:18
Alignment explanation
Indices: 55474640--55474679 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
55474630 CAGGTGCGTT
*
55474640 TCCTAACCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
55474658 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
55474676 TCCT
1 TCCT
55474680 TTTCCGAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.05, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:55475243 original size:7 final size:7
Alignment explanation
Indices: 55475220--55475273 Score: 58
Period size: 7 Copynumber: 8.0 Consensus size: 7
55475210 TTTAATTGAC
55475220 AAACCCT
1 AAACCCT
**
55475227 AAACTTT
1 AAACCCT
55475234 AAACCCT
1 AAACCCT
55475241 AAACCCT
1 AAACCCT
*
55475248 -AACCAT
1 AAACCCT
*
55475254 AAACCGT
1 AAACCCT
55475261 AAACCCT
1 AAACCCT
55475268 -AACCCT
1 AAACCCT
55475274 TAATTTAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
6 11 0.28
7 28 0.72
ACGTcount: A:0.43, C:0.37, G:0.02, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:55475258 original size:20 final size:20
Alignment explanation
Indices: 55475233--55475271 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
55475223 CCCTAAACTT
55475233 TAAACCCTAAACCCTAACCA
1 TAAACCCTAAACCCTAACCA
*
55475253 TAAACCGTAAACCCTAACC
1 TAAACCCTAAACCCTAACC
55475272 CTTAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.38, G:0.03, T:0.15
Consensus pattern (20 bp):
TAAACCCTAAACCCTAACCA
Found at i:55475287 original size:21 final size:22
Alignment explanation
Indices: 55475261--55475303 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
55475251 CATAAACCGT
55475261 AAACCCT-AACCCTTAATTTAA
1 AAACCCTAAACCCTTAATTTAA
55475282 AAACCCTAAACCCTTAATTTAA
1 AAACCCTAAACCCTTAATTTAA
55475304 CTTAAAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (22 bp):
AAACCCTAAACCCTTAATTTAA
Found at i:55475292 original size:28 final size:28
Alignment explanation
Indices: 55475233--55475406 Score: 83
Period size: 27 Copynumber: 6.5 Consensus size: 28
55475223 CCCTAAACTT
* * *
55475233 TAAACCCTAAACCC-TAAC-CATAAACCG
1 TAAACCCT-AACCCTTAACTTAAAAACCC
*
55475260 TAAACCCTAACCCTTAATTTAAAAACCC
1 TAAACCCTAACCCTTAACTTAAAAACCC
*
55475288 TAAACCCTTAA--TTTAACTTAAAAACCCC
1 TAAACCC-TAACCCTTAACTTAAAAA-CCC
* *
55475316 TTAACCCTAAACCC-TAACCCTT---AA-CT
1 TAAACCCT-AACCCTTAA--CTTAAAAACCC
* * *
55475342 TAAAACCCTAATCCTTAACTTTAAAACCG
1 T-AAACCCTAACCCTTAACTTAAAAACCC
55475371 TAAA--C----CCTTAACTTAAAAACCC
1 TAAACCCTAACCCTTAACTTAAAAACCC
55475393 T-AACCCTAACCCTT
1 TAAACCCTAACCCTT
55475407 GACTGGTACT
Statistics
Matches: 112, Mismatches: 14, Indels: 42
0.67 0.08 0.25
Matches are distributed among these distances:
21 2 0.02
22 16 0.14
23 1 0.01
25 3 0.03
26 12 0.11
27 36 0.32
28 31 0.28
29 8 0.07
31 3 0.03
ACGTcount: A:0.41, C:0.33, G:0.01, T:0.25
Consensus pattern (28 bp):
TAAACCCTAACCCTTAACTTAAAAACCC
Found at i:55475338 original size:20 final size:21
Alignment explanation
Indices: 55475313--55475403 Score: 100
Period size: 20 Copynumber: 4.4 Consensus size: 21
55475303 ACTTAAAAAC
*
55475313 CCCTTAACCCT-AAACCCTAA
1 CCCTTAACCTTAAAACCCTAA
55475333 CCCTTAA-CTTAAAACCCTAA
1 CCCTTAACCTTAAAACCCTAA
* * *
55475353 TCCTTAACTTTAAAACCGTAAA
1 CCCTTAACCTTAAAACCCT-AA
55475375 CCCTTAA-CTTAAAAACCCTAA
1 CCCTTAACCTT-AAAACCCTAA
55475396 CCC-TAACC
1 CCCTTAACC
55475404 CTTGACTGGT
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.03
20 25 0.42
21 17 0.29
22 15 0.25
ACGTcount: A:0.38, C:0.36, G:0.01, T:0.24
Consensus pattern (21 bp):
CCCTTAACCTTAAAACCCTAA
Found at i:55475376 original size:63 final size:61
Alignment explanation
Indices: 55475255--55475399 Score: 145
Period size: 63 Copynumber: 2.3 Consensus size: 61
55475245 CCTAACCATA
* * *
55475255 AACCGTAAACCCTAACCCTTAATTTAAAAACCCTAAACCCTTAATTTAACTTAAAAACCCCTT
1 AACCCTAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAATTTAACGT-AAAA-CCCTT
*
55475318 AACCCTAAACCCTAACCCTTAACTT-AAAACCCT-AATCCTTAACTTTAAAACCGT-AAACCCTT
1 AACCCTAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAA-TTT--AA-CGTAAAACCCTT
*
55475380 AA-CTTAAAAACCCTAACCCT
1 AACCCT--AAACCCTAACCCT
55475400 AACCCTTGAC
Statistics
Matches: 71, Mismatches: 5, Indels: 12
0.81 0.06 0.14
Matches are distributed among these distances:
61 10 0.14
62 18 0.25
63 39 0.55
64 2 0.03
65 2 0.03
ACGTcount: A:0.41, C:0.32, G:0.01, T:0.26
Consensus pattern (61 bp):
AACCCTAAACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAATTTAACGTAAAACCCTT
Found at i:55475382 original size:22 final size:21
Alignment explanation
Indices: 55475261--55475399 Score: 115
Period size: 21 Copynumber: 6.6 Consensus size: 21
55475251 CATAAACCGT
55475261 AAACCCTAACCCTTAA-TTTAA
1 AAACCCTAACCCTTAACTTT-A
55475282 AAACCCTAAACCCTTAA-TTTA
1 AAACCCT-AACCCTTAACTTTA
****** **
55475303 ACTTAAAAACCCCTTAACCCT-
1 AAACCCTAA-CCCTTAACTTTA
55475324 AAACCCTAACCCTTAAC-TTA
1 AAACCCTAACCCTTAACTTTA
*
55475344 AAACCCTAATCCTTAACTTTA
1 AAACCCTAACCCTTAACTTTA
* *
55475365 AAACCGTAAACCCTTAACTTAA
1 AAACCCT-AACCCTTAACTTTA
55475387 AAACCCTAACCCT
1 AAACCCTAACCCT
55475400 AACCCTTGAC
Statistics
Matches: 92, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
19 1 0.01
20 26 0.28
21 34 0.37
22 31 0.34
ACGTcount: A:0.41, C:0.32, G:0.01, T:0.26
Consensus pattern (21 bp):
AAACCCTAACCCTTAACTTTA
Found at i:55478892 original size:126 final size:126
Alignment explanation
Indices: 55478483--55478928 Score: 646
Period size: 126 Copynumber: 3.5 Consensus size: 126
55478473 CCAAAATATG
* * * **
55478483 CTACTGTAGCAAAAGCATGTCCATGTGGGCGCGATTTCACAAATTCTTCTCAATATCGCATCCTG
1 CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTC-ATAAAGCATCCTG
* *
55478548 CTTGAAGCA-TTTTTATACTATTTGCTTAGAAACTTCAAGTCGAAATTAATTT-TTCCAGGAC
65 CTTGAAGCATTTTTTATACTATTTGCTCAGAAACATCAAGTCGAAATT-ATTTCTTCCAGGAC
* * *
55478609 CTATTGTAGCAAAAGCACGTCCATGAGGGCGTGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * *
55478674 TTGAAGCATTTTTTTAAACTATTTGCTCAGAAACATGAAGTCAAAATTATTTCTTCCAGGAC
66 TTGAAGCA-TTTTTTATACTATTTGCTCAGAAACATCAAGTCGAAATTATTTCTTCCAGGAC
* *
55478736 CTACTATAGCAACAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
55478801 TTGAAGCATTTTTTATACTATTTGCTCAGAAACATCAAGTCGAAATTATTTCTTCCAGGA-
66 TTGAAGCATTTTTTATACTATTTGCTCAGAAACATCAAGTCGAAATTATTTCTTCCAGGAC
* * * * * *
55478861 CTAACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAGAAATTCTTCTGATAAAGCATCCTG
1 CT-ACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTG
55478926 CTT
65 CTT
55478929 TGATTTTTAT
Statistics
Matches: 289, Mismatches: 27, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
125 22 0.08
126 157 0.54
127 110 0.38
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (126 bp):
CTACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TTGAAGCATTTTTTATACTATTTGCTCAGAAACATCAAGTCGAAATTATTTCTTCCAGGAC
Found at i:55479090 original size:9 final size:9
Alignment explanation
Indices: 55479045--55479074 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
55479035 TTTTTTCTTT
55479045 AAAACCCTA
1 AAAACCCTA
*
55479054 AAAATCCTA
1 AAAACCCTA
55479063 AAAACCCTA
1 AAAACCCTA
55479072 AAA
1 AAA
55479075 CCTAACCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (9 bp):
AAAACCCTA
Found at i:55479095 original size:21 final size:22
Alignment explanation
Indices: 55479059--55479100 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
55479049 CCCTAAAAAT
*
55479059 CCTAAAAACCCTAAAACCTAAC
1 CCTAAAAACCCAAAAACCTAAC
55479081 CCTAAAAA-CCAAAAACCTAA
1 CCTAAAAACCCAAAAACCTAA
55479101 TGGGGAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.55, C:0.33, G:0.00, T:0.12
Consensus pattern (22 bp):
CCTAAAAACCCAAAAACCTAAC
Found at i:55480217 original size:16 final size:16
Alignment explanation
Indices: 55480192--55480222 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55480182 GTCTAGTCCC
*
55480192 ATGTGTTGTCAATCCG
1 ATGTGCTGTCAATCCG
55480208 ATGTGCTGTCAATCC
1 ATGTGCTGTCAATCC
55480223 ATTCAATCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (16 bp):
ATGTGCTGTCAATCCG
Found at i:55481051 original size:21 final size:21
Alignment explanation
Indices: 55481010--55481053 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
55481000 AGATGCTAAC
*
55481010 AAGGTAGCTCATGTACTTGCA
1 AAGGTAGCTCATGTACATGCA
*
55481031 AAGGTAGCCTTAT-TACATGCA
1 AAGGTAG-CTCATGTACATGCA
55481052 AA
1 AA
55481054 CCACACTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (21 bp):
AAGGTAGCTCATGTACATGCA
Found at i:55485623 original size:21 final size:21
Alignment explanation
Indices: 55485597--55485637 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
55485587 TTTATTACAC
55485597 GGTTGTGTAACCCTTCCACAT
1 GGTTGTGTAACCCTTCCACAT
*
55485618 GGTTGTGTAGCCCTTCCACA
1 GGTTGTGTAACCCTTCCACA
55485638 CGACTTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.29, G:0.22, T:0.32
Consensus pattern (21 bp):
GGTTGTGTAACCCTTCCACAT
Found at i:55485931 original size:143 final size:143
Alignment explanation
Indices: 55485673--55485958 Score: 572
Period size: 143 Copynumber: 2.0 Consensus size: 143
55485663 GGCCACACGG
55485673 TCGTGTGACCCCTTTTTTACAATTTTACGTTGAATTTTTTAAATTGTTCAATTTAGTCCTTAAAT
1 TCGTGTGACCCCTTTTTTACAATTTTACGTTGAATTTTTTAAATTGTTCAATTTAGTCCTTAAAT
55485738 AATCCCTGAACTATTTTTAGAGATTTTATTCACTCAATTGAGCCCCTGATAATATGAACATTTTA
66 AATCCCTGAACTATTTTTAGAGATTTTATTCACTCAATTGAGCCCCTGATAATATGAACATTTTA
55485803 GAATCCATGATCT
131 GAATCCATGATCT
55485816 TCGTGTGACCCCTTTTTTACAATTTTACGTTGAATTTTTTAAATTGTTCAATTTAGTCCTTAAAT
1 TCGTGTGACCCCTTTTTTACAATTTTACGTTGAATTTTTTAAATTGTTCAATTTAGTCCTTAAAT
55485881 AATCCCTGAACTATTTTTAGAGATTTTATTCACTCAATTGAGCCCCTGATAATATGAACATTTTA
66 AATCCCTGAACTATTTTTAGAGATTTTATTCACTCAATTGAGCCCCTGATAATATGAACATTTTA
55485946 GAATCCATGATCT
131 GAATCCATGATCT
55485959 GATTGATTGA
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
143 143 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (143 bp):
TCGTGTGACCCCTTTTTTACAATTTTACGTTGAATTTTTTAAATTGTTCAATTTAGTCCTTAAAT
AATCCCTGAACTATTTTTAGAGATTTTATTCACTCAATTGAGCCCCTGATAATATGAACATTTTA
GAATCCATGATCT
Found at i:55486693 original size:17 final size:19
Alignment explanation
Indices: 55486671--55486713 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
55486661 ATGGAAACAT
55486671 AATCTT-CA-AGGATATGC
1 AATCTTACATAGGATATGC
*
55486688 AATCTTACATATGATATGC
1 AATCTTACATAGGATATGC
55486707 AATCTTA
1 AATCTTA
55486714 GAAGATATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 2 0.09
19 15 0.65
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (19 bp):
AATCTTACATAGGATATGC
Found at i:55486724 original size:22 final size:22
Alignment explanation
Indices: 55486681--55486746 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
55486671 AATCTTCAAG
*
55486681 GATATGCAATCTT---ACATAT
1 GATATGCAATCTTAGAAAATAT
*
55486700 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAAATAT
55486722 GATATGCAATCTTAGAAAATAT
1 GATATGCAATCTTAGAAAATAT
55486744 GAT
1 GAT
55486747 TTTGTAATCT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
19 13 0.31
22 29 0.69
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (22 bp):
GATATGCAATCTTAGAAAATAT
Found at i:55487468 original size:27 final size:26
Alignment explanation
Indices: 55487438--55487512 Score: 64
Period size: 27 Copynumber: 2.8 Consensus size: 26
55487428 GTATATTTAT
55487438 ATATTTTATTTTTTATAATTCACATAC
1 ATATTTTATTTTTTATAATT-ACATAC
* *
55487465 ATA-TATATTTTTCT-TATATGTACATAT
1 ATATTTTATTTTT-TATA-AT-TACATAC
*
55487492 ATATATTTATATTTTATAATT
1 ATAT-TTTATTTTTTATAATT
55487513 TTTATCTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
26 10 0.26
27 15 0.39
28 4 0.11
29 9 0.24
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (26 bp):
ATATTTTATTTTTTATAATTACATAC
Found at i:55489306 original size:18 final size:17
Alignment explanation
Indices: 55489283--55489316 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
55489273 TATCTCTTCT
55489283 TTTGCATTCATGGCATTC
1 TTTGCATTCAT-GCATTC
55489301 TTTGCATTCATGCATT
1 TTTGCATTCATGCATT
55489317 AGCTTTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.47
Consensus pattern (17 bp):
TTTGCATTCATGCATTC
Found at i:55492134 original size:45 final size:45
Alignment explanation
Indices: 55492078--55493859 Score: 1540
Period size: 45 Copynumber: 40.0 Consensus size: 45
55492068 CAGTTAAAAC
* * * *
55492078 AGCAGATCTTGTCTTCCTGTATTAGCAGCGAAGAAGAT-AAAAACT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA-T
* * *
55492123 AGTAGATCTTGTCTTCCTGTATTAGCAGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * *
55492168 AGCAGATCTTGTCTTCCTGTACTGGCAGTGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * * *
55492213 AGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATTGAAAAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * * *
55492258 AACAGATCTTGTCTTCCTCTATCGGCAGCGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* *
55492303 AGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* *
55492348 AGCAAATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * *
55492393 AGCAGATCTTGTCTTTCTGTATTGGCAGCGAAGTAGATCAAAAAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * *
55492438 AGCAGATCTTGTCTTCCTGTATTGGTAGTGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * * * *
55492483 AGAATATCTTGTCTTCCTGTACTCGTAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * * * *
55492528 AACAGATATTGTCTTCATGTATCGGCTA-CGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGC-AGCGAAGTAGATCGAAGAT
* *
55492573 AGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* *
55492618 AGCAGATCTTGTCTTCTTGTATTGGCAGCGAATTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * *
55492663 AACAGATCTTGTCTTCCTATATTGGCATCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * *
55492708 AGCAGATCTTGTCTTCTTGTATTGGTAGCAAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * *
55492753 AGCAGATCTTGTCTACCTGTATTGGCAGAGAAGCAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * *
55492798 AGCATATCTTGTCTTTCTGTATTGGCTGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* *
55492843 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAATTAGATCGAATAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* *
55492888 AGCAGATCTTGTCTTCCTGTATTGGCAACAAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* *
55492933 AGCATATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
*
55492978 AGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * *
55493023 AGCAGATCTTGTCTTCCTATATTGACAGCAAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * *** * * * * ** *
55493068 A-CA-AGCCTTGTCTCCCTG-AGCAGTAGTGGAGTAGGTTAAAAAT
1 AGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
**
55493111 AGCAGATCTTGTCTTCCTGTATTGGCAGTAAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * *** * * * * *
55493156 A-CA-AGCCTTGTCTCCCTG-AGCAGTAGTGAAGTAGGTTGAAAAT
1 AGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
*
55493199 AACAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * * * * * ** *
55493244 A-CA-AGCCTTGTC-T-CTCTA-AGCAGCAGTGGAGTAGGTTAAAAAT
1 AGCAGA-TCTTGTCTTCCTGTATTG--GCAGCGAAGTAGATCGAAGAT
* * * *
55493287 AGCCGATCTTATCCTCCTGTATTGGCAGCGAAGTAGATCGAAGAC
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
** * *** * * * * *
55493332 CTCAG-CCTTGTC-TCCT-TGAGCAGCAGTGGAGTAGGTTGAAAAT
1 AGCAGATCTTGTCTTCCTGT-ATTGGCAGCGAAGTAGATCGAAGAT
* * *
55493375 AACAGATATTGTCTTTCTGTATTGG-AGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * * *** * * * * *
55493419 ACCA-ACCTTATCTTCCTG-AGCAGCAGTGGAGTAGGTTGAAAAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* *
55493462 AGCAGATCTTGTCTTCCTGTATGGGCAGCGAAGTAGATTGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * * * *** * * * * *
55493507 ATCAGCT-TTATCTCCCTG-AGCAGCAGTGGAGTAGGTTGAAAAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * * * * * *
55493550 AACATATCTTATCTTCCTGTATTCGTAGCGAAATAGATCGAAGAC
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
** * * * * * * ** *
55493595 CCCAG-CCTTATC-TCC-CTA--GGCAGTAGTGGAGTAGGTTAAAAAT
1 AGCAGATCTTGTCTTCCTGTATTGGC---AGCGAAGTAGATCGAAGAT
* *
55493638 AACAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * * * * * * * * * *
55493683 AGCA-AGTCCTATCTCCCTG-AGTAGCAGTGGAGTAGGTTGAAAAG
1 AGCAGA-TCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * * * *
55493727 AGCAAATCTTGTCTTTCTGTACTGACAGCGAAGCAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * * *
55493772 AGCA-AGTCTTATCTCCCTG-AGTT-GCAGCGGAGCAGA-CTGAAGAT
1 AGCAGA-TCTTGTCTTCCTGTA-TTGGCAGCGAAGTAGATC-GAAGAT
* * * *
55493816 AGTAGATCTTGTCTTCCTGTATTGGTAGTGAAGCAGATCGAAGA
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGA
55493860 CACCAGCCTT
Statistics
Matches: 1377, Mismatches: 314, Indels: 92
0.77 0.18 0.05
Matches are distributed among these distances:
40 1 0.00
41 1 0.00
42 9 0.01
43 142 0.10
44 201 0.15
45 1007 0.73
46 12 0.01
47 1 0.00
48 3 0.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (45 bp):
AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
Found at i:55493122 original size:44 final size:43
Alignment explanation
Indices: 55493074--55493568 Score: 135
Period size: 44 Copynumber: 11.3 Consensus size: 43
55493064 AGATACAAGC
* *
55493074 CTTGTCTCCCTGAGCAGTAGTGGAGTAGGTTAAAAATAGCAGAT
1 CTTGTCTCCCTGAGCAGTAGTGAAGTAGGTTGAAAATA-CAGAT
* *** * * * * * *
55493118 CTTGTCTTCCTGTATTGGCAGTAAAGTAGATCGAAGATACA-AGC
1 CTTGTCTCCCTG-AGCAGTAGTGAAGTAGGTTGAAAATACAGA-T
55493162 CTTGTCTCCCTGAGCAGTAGTGAAGTAGGTTGAAAATAACAGAT
1 CTTGTCTCCCTGAGCAGTAGTGAAGTAGGTTGAAAAT-ACAGAT
* *** * * * * * *
55493206 CTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGATACA-AGC
1 CTTGTCTCCCTG-AGCAGTAGTGAAGTAGGTTGAAAATACAGA-T
* * * * * *
55493250 CTTGTCTCTCTAAGCAGCAGTGGAGTAGGTTAAAAATAGCCGAT
1 CTTGTCTCCCTGAGCAGTAGTGAAGTAGGTTGAAAATA-CAGAT
* *** * * * * * *
55493294 CTTATC-CTCCTGTATTGGCAGCGAAGTAGATCGAAGACCT-CAG-C
1 CTTGTCTC-CCTG-AGCAGTAGTGAAGTAGGTTGAA-A-ATACAGAT
* * *
55493338 CTTGTCTCCTTGAGCAGCAGTGGAGTAGGTTGAAAATAACAGAT
1 CTTGTCTCCCTGAGCAGTAGTGAAGTAGGTTGAAAAT-ACAGAT
* ** ** * * * * * *
55493382 ATTGTCTTTCTGTA-TTGGAGCGAAGTAGATCGAAGATACCA-AC
1 CTTGTCTCCCTG-AGCAGTAGTGAAGTAGGTTGAAAATA-CAGAT
* * * *
55493425 CTTATCTTCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTCCCTGAGCAGTAGTGAAGTAGGTTGAAAATA-CAGAT
* * * * * * *
55493469 CTTGTCTTCCTGTATG-GGCAGCGAAGTAGATTGAAGATATCAGCT
1 CTTGTCTCCCTG-A-GCAGTAGTGAAGTAGGTTGAAAATA-CAGAT
* * * *
55493514 -TTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAACATAT
1 CTTGTCTCCCTGAGCAGTAGTGAAGTAGGTTGAAAAT-ACAGAT
* *
55493557 CTTATCTTCCTG
1 CTTGTCTCCCTG
55493569 TATTCGTAGC
Statistics
Matches: 311, Mismatches: 115, Indels: 50
0.65 0.24 0.11
Matches are distributed among these distances:
41 1 0.00
42 3 0.01
43 105 0.34
44 123 0.40
45 76 0.24
46 2 0.01
47 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (43 bp):
CTTGTCTCCCTGAGCAGTAGTGAAGTAGGTTGAAAATACAGAT
Found at i:55493546 original size:43 final size:44
Alignment explanation
Indices: 55493082--55493568 Score: 177
Period size: 43 Copynumber: 11.1 Consensus size: 44
55493072 GCCTTGTCTC
* * *
55493082 CCTGAGCAGTAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTT
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTATCTT
*** ** * * * * * *
55493126 CCTGTATTGGCAGTAAAGTAGATCGAAGATA-CA-AGCCTTGTCTC
1 CCTG-AGCAGCAGTGGAGTAGGTTGAAAATAGCAGA-TCTTATCTT
* * * *
55493170 CCTGAGCAGTAGTGAAGTAGGTTGAAAATAACAGATCTTGTCTT
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTATCTT
*** * * * * * * *
55493214 CCTGTATTGGCAGCGAAGTAGATCGAAGATA-CA-AGCCTTGTC-T
1 CCTG-AGCAGCAGTGGAGTAGGTTGAAAATAGCAGA-TCTTATCTT
* * * *
55493257 CTCTAAGCAGCAGTGGAGTAGGTTAAAAATAGCCGATCTTATCCT
1 C-CTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTATCTT
*** * * * * * *** * *
55493302 CCTGTATTGGCAGCGAAGTAGATCGAAGACCTCAG-CCTTGTC-T
1 CCTG-AGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTATCTT
* * *
55493345 CCTTGAGCAGCAGTGGAGTAGGTTGAAAATAACAGATATTGTCTT
1 CC-TGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTATCTT
* ** * * * * * * * *
55493390 TCTGTA-TTGGAGCGAAGTAGATCGAAGATACCA-ACCTTATCTT
1 CCTG-AGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTATCTT
*
55493433 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTT
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTATCTT
* * * * * * * *
55493477 CCTGTATG-GGCAGCGAAGTAGATTGAAGATATCAGCT-TTATCTC
1 CCTG-A-GCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTATCTT
* *
55493521 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAACATATCTTATCTT
1 CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTATCTT
55493565 CCTG
1 CCTG
55493569 TATTCGTAGC
Statistics
Matches: 306, Mismatches: 116, Indels: 42
0.66 0.25 0.09
Matches are distributed among these distances:
42 2 0.01
43 111 0.36
44 111 0.36
45 81 0.26
46 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
CCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTATCTT
Found at i:55493806 original size:44 final size:44
Alignment explanation
Indices: 55493662--55493817 Score: 127
Period size: 44 Copynumber: 3.5 Consensus size: 44
55493652 TCCTATATTG
* * *
55493662 GCAGCGAAGTAGATCGAAGATAGCAAGTCCTATCTCCCTGAGTA
1 GCAGCGAAGCAGATCGAAGATAGCAAGTCTTATCTCCCTGAGTT
* * * * * * * * * ** *
55493706 GCAGTGGAGTAGGTTGAAAAGAGCAAATCTTGTCTTTCTGTA-CT
1 GCAGCGAAGCAGATCGAAGATAGCAAGTCTTATCTCCCTG-AGTT
55493750 GACAGCGAAGCAGATCGAAGATAGCAAGTCTTATCTCCCTGAGTT
1 G-CAGCGAAGCAGATCGAAGATAGCAAGTCTTATCTCCCTGAGTT
*
55493795 GCAGCGGAGCAGA-CTGAAGATAG
1 GCAGCGAAGCAGATC-GAAGATAG
55493818 TAGATCTTGT
Statistics
Matches: 82, Mismatches: 26, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
43 1 0.01
44 50 0.61
45 31 0.38
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (44 bp):
GCAGCGAAGCAGATCGAAGATAGCAAGTCTTATCTCCCTGAGTT
Found at i:55493894 original size:89 final size:89
Alignment explanation
Indices: 55493631--55493945 Score: 276
Period size: 89 Copynumber: 3.5 Consensus size: 89
55493621 TGGAGTAGGT
* * * * * * * *
55493631 TAAAAATAACAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAAGTCC-TAT
1 TAAAAACATCAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAGACAGCAAG-CCTTAC
* ** * **
55493695 CTCCCTGAGTAGCAGTGGAGTAGGT
65 CTCCCTGAGTTGCAGCAGAGCAGAC
* * * * * * * * * *
55493720 TGAAAAGAGCAAATCTTGTCTTTCTGTACTGACAGCGAAGCAGATCGAAGATAGCAAGTCTTATC
1 TAAAAACATCAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAGACAGCAAGCCTTACC
*
55493785 TCCCTGAGTTGCAGCGGAGCAGAC
66 TCCCTGAGTTGCAGCAGAGCAGAC
* * * * * * *
55493809 TGAAGATAGT-AGATCTTGTCTTCCTGTATTGGTAGTGAAGCAGATCGAAGACA-CCAGCCTTGC
1 TAAAAACA-TCAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAGACAGCAAGCCTTAC
*
55493872 CTCCCTGAGTTTGTAGCAGAGCAGAC
65 CTCCCTGAG-TTGCAGCAGAGCAGAC
*
55493898 TAAAAACATCAGATCTTATCTTCCTGTACTGGCAGTGAAGCAGATCGA
1 TAAAAACATCAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGA
55493946 GAACACTAGT
Statistics
Matches: 185, Mismatches: 37, Indels: 8
0.80 0.16 0.03
Matches are distributed among these distances:
88 17 0.09
89 168 0.91
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (89 bp):
TAAAAACATCAGATCTTGTCTTCCTGTACTGGCAGTGAAGCAGATCGAAGACAGCAAGCCTTACC
TCCCTGAGTTGCAGCAGAGCAGAC
Found at i:55494195 original size:131 final size:132
Alignment explanation
Indices: 55493953--55494214 Score: 377
Period size: 131 Copynumber: 2.0 Consensus size: 132
55493943 CGAGAACACT
* *
55493953 AGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGTCGAAAATTGTAGATCCTGTCTCCCTAAGCAGT
1 AGTCATATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAAATTGTAGATCCTGTCTCCCTAAGCAGT
* * * *
55494018 AGTGGAGTAGATCGAAGACGGCGAATCTTATCTTCCCGAGATAGTA-GGAAGAAGATTTAAGCCA
66 AGTGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCGAGAGAGTAGGGAAGAAGATTTAAACCA
55494082 CC
131 CC
* * *
55494084 AGTCATATCTCTCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCTCC-AAGCAG
1 AGTCATATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAAATTGTAGATCCTGTCTC-CCTAAGCAG
* * *
55494148 TAGTGGAGCAGATCAAAGACGGCGAGTCTTATCTTCCTGA-AGGAGTAGGGAAGCAGATTTAAAC
65 TAGTGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCGAGA-GAGTAGGGAAGAAGATTTAAAC
55494212 CAC
129 CAC
55494215 TAGCCTTATT
Statistics
Matches: 116, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
130 1 0.01
131 96 0.83
132 19 0.16
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (132 bp):
AGTCATATCTCCCTGAGCAGCAGTGGAGTAGGTCGAAAATTGTAGATCCTGTCTCCCTAAGCAGT
AGTGGAGCAGATCAAAGACGGCGAATCTTATCTTCCCGAGAGAGTAGGGAAGAAGATTTAAACCA
CC
Found at i:55494705 original size:19 final size:19
Alignment explanation
Indices: 55494681--55494734 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
55494671 AATCTTCAAG
55494681 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
55494700 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
55494719 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
55494735 AAATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:55495050 original size:15 final size:16
Alignment explanation
Indices: 55495024--55495056 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
55495014 TTTTCCCTTA
55495024 TTATTCATTTTCAAAT
1 TTATTCATTTTCAAAT
55495040 TTATT-ATTTTCAAAT
1 TTATTCATTTTCAAAT
55495055 TT
1 TT
55495057 GTTTACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTCATTTTCAAAT
Found at i:55497854 original size:10 final size:10
Alignment explanation
Indices: 55497841--55497913 Score: 69
Period size: 10 Copynumber: 7.5 Consensus size: 10
55497831 TTTTGATGTA
55497841 TTTTATAATT
1 TTTTATAATT
*
55497851 TTTTATGA-T
1 TTTTATAATT
**
55497860 TTTTATAAAA
1 TTTTATAATT
*
55497870 TTTTACAATT
1 TTTTATAATT
*
55497880 TTTTCTAATT
1 TTTTATAATT
* *
55497890 TTTAATAAAT
1 TTTTATAATT
55497900 TTTT-TAATT
1 TTTTATAATT
55497909 TTTTA
1 TTTTA
55497914 ATTAAAATTT
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
9 16 0.33
10 32 0.67
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:55497863 original size:19 final size:19
Alignment explanation
Indices: 55497841--55497913 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
55497831 TTTTGATGTA
*
55497841 TTTTATAATTTTTTATGAT
1 TTTTATAATTTTTTATAAT
** *
55497860 TTTTATAAAATTTTACAATT
1 TTTTATAATTTTTTATAA-T
* *
55497880 TTTTCTAATTTTTAATAAAT
1 TTTTATAATTTTTTAT-AAT
55497900 TTTT-TAATTTTTTA
1 TTTTATAATTTTTTA
55497914 ATTAAAATTT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 23 0.55
20 17 0.40
21 2 0.05
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTTATAAT
Found at i:55497872 original size:29 final size:29
Alignment explanation
Indices: 55497840--55497913 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
55497830 TTTTTGATGT
*
55497840 ATTTTATAATTTTTTATGATTTTT-ATAAA
1 ATTTTATAATTTTTTATAATTTTTAAT-AA
* *
55497869 ATTTTACAATTTTTTCTAATTTTTAATAA
1 ATTTTATAATTTTTTATAATTTTTAATAA
*
55497898 ATTTTTTAATTTTTTA
1 ATTTTATAATTTTTTA
55497914 ATTAAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 36 0.95
30 2 0.05
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (29 bp):
ATTTTATAATTTTTTATAATTTTTAATAA
Found at i:55498196 original size:88 final size:87
Alignment explanation
Indices: 55498074--55498311 Score: 300
Period size: 88 Copynumber: 2.7 Consensus size: 87
55498064 TCAAGAACTC
* *
55498074 AATTGAGTG-AAAAAAAGTAGGGGCTTAATAGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTGAT
1 AATTGAGTGCAAAAAAAGCAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGG-CTTTTTGAT
* *
55498138 GCATTTTGAAAATTTAAGTACCCA
65 ACATTTTGAAAATTCAAGTA-CCA
* * *
55498162 AATTGAGTGCAAAAAAAG-GGGGGCTTAATTGCTTTTTCTGAAAAAGTTTGAGAGCCTTTTTGAT
1 AATTGAGTGCAAAAAAAGCAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAG-GGCTTTTTGAT
* ***
55498226 ACATTTTGAAAGTTCAAGTATGT
65 ACATTTTGAAAATTCAAGTACCA
**
55498249 AATTGAGTGCATAAAAAGAGCAGGGGCTTAATTTTTTTTTTTGAAAAAGTTTGAGGGCTTTTT
1 AATTGAGTGCA-AAAAA-AGCAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGCTTTTT
55498312 ACACCCTTAA
Statistics
Matches: 130, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
87 11 0.08
88 71 0.55
89 18 0.14
90 30 0.23
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.37
Consensus pattern (87 bp):
AATTGAGTGCAAAAAAAGCAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGCTTTTTGATA
CATTTTGAAAATTCAAGTACCA
Found at i:55508607 original size:32 final size:32
Alignment explanation
Indices: 55508570--55508646 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
55508560 ATGCATGTGT
* * **
55508570 GTAACTTTTCATCTTCAAGTCTCTTTGCATTA
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
* * *
55508602 TTAACTCTTCATATTCAAGCCTCTTCACATTC
1 GTAACTTTTCATATTCAAGCCTCTTCACATTA
55508634 GTAACTTTTCATA
1 GTAACTTTTCATA
55508647 ATTTATTTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.06, T:0.44
Consensus pattern (32 bp):
GTAACTTTTCATATTCAAGCCTCTTCACATTA
Found at i:55515268 original size:137 final size:137
Alignment explanation
Indices: 55515022--55515298 Score: 518
Period size: 137 Copynumber: 2.0 Consensus size: 137
55515012 ATGAAAGTAA
* *
55515022 ATAAACTAAATAAAATATACTTATAATTGAATTAGTGGAAGAAAAAGATGAAAGATATCTTCTTC
1 ATAAACTAAATAAAATATACTTATAACTGAATTAGTGGAAGAAAAAGATGAAAGATATCATCTTC
*
55515087 TTCTTCCAAACAACGAAACAAGAGAAGGAAAAGCTAAAGAAAACTTCAAGGTATTTGGCCTTAAT
66 TTCTTCCAAACAACGAAACAAGAGAAGGAAAACCTAAAGAAAACTTCAAGGTATTTGGCCTTAAT
55515152 TTATATT
131 TTATATT
*
55515159 ATAAATTAAATAAAATATACTTATAACTGAATTAGTGGAAGAAAAAGATGAAAGATATCATCTTC
1 ATAAACTAAATAAAATATACTTATAACTGAATTAGTGGAAGAAAAAGATGAAAGATATCATCTTC
55515224 TTCTTCCAAACAACGAAACAAGAGAAGGAAAACCTAAAGAAAACTTCAAGGTATTTGGCCTTAAT
66 TTCTTCCAAACAACGAAACAAGAGAAGGAAAACCTAAAGAAAACTTCAAGGTATTTGGCCTTAAT
55515289 TTATATT
131 TTATATT
55515296 ATA
1 ATA
55515299 CTATTACTGA
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 136 1.00
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (137 bp):
ATAAACTAAATAAAATATACTTATAACTGAATTAGTGGAAGAAAAAGATGAAAGATATCATCTTC
TTCTTCCAAACAACGAAACAAGAGAAGGAAAACCTAAAGAAAACTTCAAGGTATTTGGCCTTAAT
TTATATT
Found at i:55522922 original size:15 final size:15
Alignment explanation
Indices: 55522902--55522936 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
55522892 TCTCTAGAAA
55522902 TCTTCTAAAATAATT
1 TCTTCTAAAATAATT
*
55522917 TCTTCTGAAATAATT
1 TCTTCTAAAATAATT
55522932 TCTTC
1 TCTTC
55522937 AGAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.49
Consensus pattern (15 bp):
TCTTCTAAAATAATT
Found at i:55522941 original size:15 final size:15
Alignment explanation
Indices: 55522909--55522941 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
55522899 AAATCTTCTA
*
55522909 AAATAATTTCTTCTG
1 AAATAATTTCTTCAG
55522924 AAATAATTTCTTCAG
1 AAATAATTTCTTCAG
55522939 AAA
1 AAA
55522942 ATTTTCTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (15 bp):
AAATAATTTCTTCAG
Found at i:55523113 original size:58 final size:60
Alignment explanation
Indices: 55523051--55523164 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 60
55523041 ATTACTTTAA
* * *
55523051 TATTAAATTAATACAACACTTA-T-CAAGATAAATACTAGATTAAATTTAATATTAAATC
1 TATTAAAGTAATACAACACTTACTACAAGATAAATACTAAATTAAACTTAATATTAAATC
* * *
55523109 TATTAAAGTAATAGAATACTTATCTACAAGATAAATATTAAATTAAACTTAATATT
1 TATTAAAGTAATACAACACTTA-CTACAAGATAAATACTAAATTAAACTTAATATT
55523165 GAGATAATCA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 19 0.40
60 1 0.02
61 27 0.57
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (60 bp):
TATTAAAGTAATACAACACTTACTACAAGATAAATACTAAATTAAACTTAATATTAAATC
Found at i:55523192 original size:20 final size:18
Alignment explanation
Indices: 55523142--55523193 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
55523132 CTACAAGATA
55523142 AATATTAAATTAA-ACTT
1 AATATTAAATTAATACTT
*
55523159 AATATTGAGA-TAATCACTTT
1 AATATT-AAATTAAT-AC-TT
55523179 AATATTAAATTAATA
1 AATATTAAATTAATA
55523194 AAATATTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 9 0.32
18 2 0.07
19 5 0.18
20 12 0.43
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (18 bp):
AATATTAAATTAATACTT
Found at i:55528021 original size:15 final size:16
Alignment explanation
Indices: 55527989--55528023 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
55527979 TAAATAATTT
55527989 TTATAAAGATTATATA
1 TTATAAAGATTATATA
*
55528005 TTATAAAG-TTTTATA
1 TTATAAAGATTATATA
55528020 TTAT
1 TTAT
55528024 TTCTTTACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (16 bp):
TTATAAAGATTATATA
Found at i:55548555 original size:23 final size:23
Alignment explanation
Indices: 55548511--55548555 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
55548501 TTATATTAAT
* * **
55548511 ATAATTTAATTAGATATTTATTA
1 ATAATTTAATTAAAAAAATATTA
55548534 ATAATTTAATTAAAAAAATATT
1 ATAATTTAATTAAAAAAATATT
55548556 GGTATAAAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATAATTTAATTAAAAAAATATTA
Found at i:55551132 original size:16 final size:16
Alignment explanation
Indices: 55551113--55551143 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
55551103 TCTAGATATT
55551113 AAAAAGAGAGTTCTGA
1 AAAAAGAGAGTTCTGA
55551129 AAAAAGAGAGTTCTG
1 AAAAAGAGAGTTCTG
55551144 GAACCTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.26, T:0.19
Consensus pattern (16 bp):
AAAAAGAGAGTTCTGA
Found at i:55557587 original size:24 final size:24
Alignment explanation
Indices: 55557560--55557605 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
55557550 TGCTAAAGAA
55557560 GGAAAGGGTTTCAGTTAAAAATGG
1 GGAAAGGGTTTCAGTTAAAAATGG
*
55557584 GGAAAGGGTTTTAGTTAAAAAT
1 GGAAAGGGTTTCAGTTAAAAAT
55557606 AAAGAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.30, T:0.28
Consensus pattern (24 bp):
GGAAAGGGTTTCAGTTAAAAATGG
Found at i:55557612 original size:24 final size:24
Alignment explanation
Indices: 55557561--55557612 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
55557551 GCTAAAGAAG
***
55557561 GAAAGGGTTTCAGTTAAAAATGGG
1 GAAAGGGTTTCAGTTAAAAATAAA
*
55557585 GAAAGGGTTTTAGTTAAAAATAAA
1 GAAAGGGTTTCAGTTAAAAATAAA
55557609 GAAA
1 GAAA
55557613 AAAATAATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.02, G:0.27, T:0.25
Consensus pattern (24 bp):
GAAAGGGTTTCAGTTAAAAATAAA
Found at i:55557951 original size:11 final size:11
Alignment explanation
Indices: 55557935--55558070 Score: 53
Period size: 11 Copynumber: 12.4 Consensus size: 11
55557925 TTTTTTTCTA
55557935 TTTATTATTAT
1 TTTATTATTAT
*
55557946 TTTATTGTTAT
1 TTTATTATTAT
*
55557957 TTTCTT-TT-T
1 TTTATTATTAT
55557966 GTTTATTATTAT
1 -TTTATTATTAT
* ***
55557978 TTTGTTGCCAT
1 TTTATTATTAT
* *
55557989 TTCATAATTAT
1 TTTATTATTAT
* *
55558000 ATTGTTATT-T
1 TTTATTATTAT
55558010 TATTATTATTAT
1 T-TTATTATTAT
* *
55558022 TTGAATATTAT
1 TTTATTATTAT
* * * * *
55558033 ATAACTCTTGT
1 TTTATTATTAT
*
55558044 TTTATTGTTAAT
1 TTTATTATT-AT
*
55558056 TTTGTTATTAT
1 TTTATTATTAT
55558067 TTTA
1 TTTA
55558071 GAGATATTTG
Statistics
Matches: 85, Mismatches: 34, Indels: 12
0.65 0.26 0.09
Matches are distributed among these distances:
9 1 0.01
10 8 0.09
11 65 0.76
12 11 0.13
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.65
Consensus pattern (11 bp):
TTTATTATTAT
Found at i:55558571 original size:17 final size:17
Alignment explanation
Indices: 55558533--55558581 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
55558523 GGGTGAGAAG
55558533 TAAAAGTTTAGGGGAAAA
1 TAAAAGTTTAGGGG-AAA
*
55558551 TAAAAAGTTTTGGGG-AA
1 T-AAAAGTTTAGGGGAAA
55558568 TAAAAGTTTGAGGG
1 TAAAAGTTT-AGGG
55558582 AAAGTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.30
17 6 0.22
18 1 0.04
19 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.27
Consensus pattern (17 bp):
TAAAAGTTTAGGGGAAA
Found at i:55562999 original size:2 final size:2
Alignment explanation
Indices: 55562992--55563017 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55562982 ATAACAAAAG
55562992 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
55563018 GAGGTGGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55573328 original size:43 final size:43
Alignment explanation
Indices: 55573004--55573326 Score: 400
Period size: 43 Copynumber: 7.5 Consensus size: 43
55572994 CCATTAAAGG
* *
55573004 TCATGACTTTTAGCGGCGCTGTTCCCACAAACGCCGTTATAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* *
55573047 TCATGACTTTTAGCGGCGCTTTTCCCACAAATC-TCGTTATAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAA-CGCCGCTATAGA
* * * *
55573090 TCATAACTTTTAGCGGTGCTGTTCCCACAAACGCCGCTACAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
55573133 TCATGACTTTTAGCGGCG-TTGTTCCCACAAACGCCGCTATAGA
1 TCATGACTTTTAGCGGCGCTT-TTCCCACAAACGCCGCTATAGA
* **
55573176 TCATGACTTTTAGCGGCGCTTCTCCCATTAACGCCGCTATAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* * *
55573219 TCATGACTTTTAGCGGCGCTTCTCCTACAAACGCCGTTATAGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* * *** *
55573262 TCATGAATTTTAGCGACGCTTTTTTTATAAACGCCGCTA-AGA
1 TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
* * *
55573304 ACATGACCTTTAGCGGCGGTTTT
1 TCATGACTTTTAGCGGCGCTTTT
55573327 TTAAAAAACA
Statistics
Matches: 245, Mismatches: 31, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
42 23 0.09
43 219 0.89
44 3 0.01
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (43 bp):
TCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGA
Found at i:55573652 original size:21 final size:21
Alignment explanation
Indices: 55573628--55573698 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
55573618 TTCTGCTCTG
*
55573628 CTCTACTTCCCTCGCTGC-AGC
1 CTCTGCTTCCCTCGCTGCTA-C
* * *
55573649 CTCTGCTTCTCTCACTGCTAT
1 CTCTGCTTCCCTCGCTGCTAC
*
55573670 CTCTGCTTCCCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTGCTAC
*
55573691 ATCTGCTT
1 CTCTGCTT
55573699 TAAGTTGTAG
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 39 0.98
22 1 0.03
ACGTcount: A:0.07, C:0.42, G:0.14, T:0.37
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCTAC
Found at i:55573851 original size:87 final size:87
Alignment explanation
Indices: 55573648--55573838 Score: 321
Period size: 87 Copynumber: 2.2 Consensus size: 87
55573638 CTCGCTGCAG
* *
55573648 CCTCTGCTTCTCTC-ACTGCTATCTCTGCTTCCCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTG
1 CCTCAGCTTCTCTCGA-TACTATCTCTGCTTCCCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTG
55573712 GAGTTCTTCATATTTTCTTTGAA
65 GAGTTCTTCATATTTTCTTTGAA
* *
55573735 CCTCAGCTTCTCTCGATACTACCTCTGCTTCCCTCGCTGTTGCATCTGCTTTAAGTTGTAGCTGG
1 CCTCAGCTTCTCTCGATACTATCTCTGCTTCCCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGG
55573800 AGTTCTTCATATTTTCTTTGAA
66 AGTTCTTCATATTTTCTTTGAA
*
55573822 CCTCGGCTTCTCTCGAT
1 CCTCAGCTTCTCTCGAT
55573839 GTTGTCTCTG
Statistics
Matches: 98, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 97 0.99
88 1 0.01
ACGTcount: A:0.13, C:0.29, G:0.16, T:0.41
Consensus pattern (87 bp):
CCTCAGCTTCTCTCGATACTATCTCTGCTTCCCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGG
AGTTCTTCATATTTTCTTTGAA
Found at i:55574540 original size:31 final size:31
Alignment explanation
Indices: 55574497--55574576 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
55574487 CATGGTTGAT
55574497 TTAGCAGCAAAAAACAATAGAAGGTACCATC
1 TTAGCAGCAAAAAACAATAGAAGGTACCATC
* * *
55574528 TTAGCAGTAAAAACCAATAGAATGTACCATC
1 TTAGCAGCAAAAAACAATAGAAGGTACCATC
* * *
55574559 GTAGCTGCAAAAACCAAT
1 TTAGCAGCAAAAAACAAT
55574577 TAAAAACCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.19
Consensus pattern (31 bp):
TTAGCAGCAAAAAACAATAGAAGGTACCATC
Found at i:55575785 original size:45 final size:46
Alignment explanation
Indices: 55575736--55575853 Score: 130
Period size: 45 Copynumber: 2.5 Consensus size: 46
55575726 ATTTGATTTA
* *
55575736 TAGTGCTTGTATTTTTCAAAAATTTTATAGTAGGAATTTAA-TCTG
1 TAGTGCTTGTATTTTTCAAAAATTTCAAAGTAGGAATTTAACTCTG
* * * *
55575781 TAGTGTTTGTATTTTTCTAAAACTTCAAATTAGGAATTTAACTCTG
1 TAGTGCTTGTATTTTTCAAAAATTTCAAAGTAGGAATTTAACTCTG
*
55575827 TGAAGTCAGGTTGTATTTTTCAAAAAT
1 T--AGT--GCTTGTATTTTTCAAAAAT
55575854 ACTAATTAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
45 35 0.59
46 5 0.08
48 3 0.05
50 16 0.27
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.45
Consensus pattern (46 bp):
TAGTGCTTGTATTTTTCAAAAATTTCAAAGTAGGAATTTAACTCTG
Found at i:55575995 original size:7 final size:7
Alignment explanation
Indices: 55575985--55576010 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55575975 TAATAACCCA
55575985 TAAACCT
1 TAAACCT
55575992 TAAACCT
1 TAAACCT
55575999 TAAACCT
1 TAAACCT
55576006 TAAAC
1 TAAAC
55576011 TCCAAGCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAACCT
Found at i:55576080 original size:14 final size:14
Alignment explanation
Indices: 55576061--55576097 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
55576051 ATAAATCATA
*
55576061 AACCCCTAACCCTT
1 AACCCCTAACACTT
55576075 AACCCCTAACACTT
1 AACCCCTAACACTT
*
55576089 AAACCCTAA
1 AACCCCTAA
55576098 GCCCCAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.38, C:0.43, G:0.00, T:0.19
Consensus pattern (14 bp):
AACCCCTAACACTT
Found at i:55576118 original size:7 final size:7
Alignment explanation
Indices: 55576103--55576141 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
55576093 CCTAAGCCCC
*
55576103 AACCTTA
1 AACCATA
55576110 AACCATA
1 AACCATA
*
55576117 AACCACA
1 AACCATA
55576124 AACCATA
1 AACCATA
*
55576131 ATCCATA
1 AACCATA
55576138 AACC
1 AACC
55576142 CTTAACCCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.15
Consensus pattern (7 bp):
AACCATA
Found at i:55576203 original size:8 final size:7
Alignment explanation
Indices: 55576186--55576289 Score: 52
Period size: 7 Copynumber: 14.6 Consensus size: 7
55576176 ACATTAACTA
55576186 TAAACCC
1 TAAACCC
55576193 TAAACCCC
1 TAAA-CCC
55576201 T-AACCC
1 TAAACCC
*
55576207 TTAACCCC
1 -TAAACCC
55576215 T-AACACC
1 TAAAC-CC
* *
55576222 TAAGCCT
1 TAAACCC
55576229 TAAACCC
1 TAAACCC
*
55576236 -CAACCC
1 TAAACCC
*
55576242 TTAAACCA
1 -TAAACCC
*
55576250 TAATCCC
1 TAAACCC
55576257 TAAACCC
1 TAAACCC
*
55576264 TTAACCC
1 TAAACCC
** *
55576271 ATATTCCT
1 -TAAACCC
55576279 TAAACCC
1 TAAACCC
55576286 TAAA
1 TAAA
55576290 TCATAGAATA
Statistics
Matches: 69, Mismatches: 20, Indels: 16
0.66 0.19 0.15
Matches are distributed among these distances:
6 10 0.14
7 42 0.61
8 17 0.25
ACGTcount: A:0.38, C:0.40, G:0.01, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:55576212 original size:21 final size:22
Alignment explanation
Indices: 55576190--55576270 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 22
55576180 TAACTATAAA
55576190 CCCTAAACCCCTAACCCTTAAC
1 CCCTAAACCCCTAACCCTTAAC
* *
55576212 CCCT-AACACCTAAGCCTTAAAC
1 CCCTAAACCCCTAACCCTT-AAC
* * * *
55576234 CCC--AACCCTTAAACCATAAT
1 CCCTAAACCCCTAACCCTTAAC
*
55576254 CCCTAAACCCTTAACCC
1 CCCTAAACCCCTAACCC
55576271 ATATTCCTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 5 0.10
21 22 0.46
22 21 0.44
ACGTcount: A:0.35, C:0.46, G:0.01, T:0.19
Consensus pattern (22 bp):
CCCTAAACCCCTAACCCTTAAC
Found at i:55576265 original size:22 final size:22
Alignment explanation
Indices: 55576237--55576294 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
55576227 CTTAAACCCC
55576237 AACCCTTAAACCATAATCCCTA
1 AACCCTTAAACCATAATCCCTA
* * *
55576259 AACCCTTAACCCATATTCCTTA
1 AACCCTTAAACCATAATCCCTA
*
55576281 AACCC-TAAATCATA
1 AACCCTTAAACCATA
55576295 GAATATATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 7 0.23
22 24 0.77
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (22 bp):
AACCCTTAAACCATAATCCCTA
Found at i:55576330 original size:39 final size:39
Alignment explanation
Indices: 55576276--55576362 Score: 140
Period size: 39 Copynumber: 2.2 Consensus size: 39
55576266 AACCCATATT
*
55576276 CCTTAAACCCTAAATCATAGAATATATATAAACCT-TAAA
1 CCTTAAACCCTAAATCATAGAACATATATAAA-CTATAAA
*
55576315 CCTTAAACCCTAAATCATAGAACATATATAAATTATAAA
1 CCTTAAACCCTAAATCATAGAACATATATAAACTATAAA
55576354 CCTTAAACC
1 CCTTAAACC
55576363 TCAACCCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
38 1 0.02
39 44 0.98
ACGTcount: A:0.48, C:0.22, G:0.02, T:0.28
Consensus pattern (39 bp):
CCTTAAACCCTAAATCATAGAACATATATAAACTATAAA
Found at i:55576425 original size:15 final size:14
Alignment explanation
Indices: 55576385--55576425 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
55576375 CAATAAACAA
*
55576385 TAAACCATAACCCC
1 TAAACCATAATCCC
55576399 TAAATCCATAATCCC
1 TAAA-CCATAATCCC
55576414 TAAACCACTAAT
1 TAAACCA-TAAT
55576426 GCGTCTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCATAATCCC
Done.